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comparison DeMeanderize.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="DeMeanderize" name="DeMeanderize" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Orders the spectra of MALDI spotting plates correctly.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="DeMeanderize" name="DeMeanderize" version="2.0.0">
5 <token name="@EXECUTABLE@">DeMeanderize</token> 5 <description>Orders the spectra of MALDI spotting plates correctly.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">DeMeanderize</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>DeMeanderize 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>DeMeanderize
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -num_spots_per_row ${param_num_spots_per_row} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_num_spots_per_row:
22 -num_spots_per_row $param_num_spots_per_row
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
16 #if $adv_opts.adv_opts_selector=='advanced': 25 #if $adv_opts.adv_opts_selector=='advanced':
17 -RT_distance ${adv_opts.param_RT_distance} 26 #if $adv_opts.param_RT_distance:
27 -RT_distance $adv_opts.param_RT_distance
28 #end if
29 #if $adv_opts.param_force:
30 -force
31 #end if
18 #end if 32 #end if
19 </command> 33 </command>
20 <inputs> 34 <inputs>
21 <param name="param_in" type="data" format="mzML" optional="False" label="Input experiment file, containing the wrongly sorted spectra." help="(-in)"/> 35 <param format="mzml" help="(-in) " label="Input experiment file, containing the wrongly sorted spectra" name="param_in" optional="False" type="data"/>
22 <param name="param_num_spots_per_row" type="integer" min="1" optional="True" value="48" label="Number of spots in one column, until next row is spotted." help="(-num_spots_per_row)"/> 36 <param help="(-num_spots_per_row) " label="Number of spots in one column, until next row is spotted" min="1" name="param_num_spots_per_row" optional="True" type="integer" value="48"/>
23 <expand macro="advanced_options"> 37 <expand macro="advanced_options">
24 <param name="param_RT_distance" type="float" min="0.0" optional="True" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT." help="(-RT_distance)"/> 38 <param help="(-RT_distance) " label="RT distance between two spots which is used to calculated pseudo RT" min="0.0" name="param_RT_distance" optional="True" type="float" value="1.0"/>
25 </expand> 39 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
26 </inputs> 40 </expand>
27 <outputs> 41 </inputs>
28 <data name="param_out" label="Output experiment file with correctly sorted spectra." format="mzML"/> 42 <outputs>
29 </outputs> 43 <data format="mzml" name="param_out"/>
30 <help>**What it does** 44 </outputs>
31 45 <help>Orders the spectra of MALDI spotting plates correctly.
32 Orders the spectra of MALDI spotting plates correctly.
33 46
34 47
35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DeMeanderize.html 48 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DeMeanderize.html</help>
36 49 </tool>
37 @REFERENCES@
38 </help>
39 </tool>